Abstract

Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.

Framework of the database construction in CircNet. The graph illustrates how the network in CircNet was constructed. For circRNA identification, transcriptome sequencing data sets were obtained from the NCBI Sequence Read Archive (SRA). The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline we developed (scripts provided on circBase). Detected back-spliced junction sites were further compared with hg19 human genome annotation to define circRNA isoforms. Only isoforms with an average expression level (those with an average FPKM in the 464 examined samples greater than 0.01) were included in the database. To predict circRNA–miRNA interactions, the occurrence of miRNA target seeds in circRNA isoforms were examined and normalized by isoform length. The significance of interactions was evaluated by referring to the background distribution of miRNA seeds in all transcripts and only circRNA–miRNA interactions with P-values < 0.001 were reported.

Overview of CircNet web interface. (A) Users can search a gene or miRNA of interest, and then CircNet generates three panels as follows: (1) the left panel: a gene–circRNA–miRNA regulatory network, (2) the top-right panel: circRNA expression profiles, circRNA–miRNA sponge regulatory network and resource of back-spliced junction sites; (3) the bottom-right panel: a genome browser for circRNAs. (B) When users click a circRNA in the left panel, CircNet shows a circRNA–gene–miRNA regulatory network centered on the given circRNA. (C) Using BLAST, users can input a DNA or RNA sequence to search for circRNA isoforms included in CircNet.